Contacts of the helix formed by residues 559 - 566 (chain B) in PDB entry 1B3U
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 559 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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521B LEU* 4.3 9.2 - - + -
525B LEU* 4.4 2.9 - - + -
543B LEU* 4.2 28.3 - - + -
547B GLY* 5.5 1.8 - - - -
550B LEU* 3.9 26.7 - - + -
555B LEU* 3.1 35.9 + - + +
558B GLU* 1.3 78.6 - - + +
560B LYS* 1.3 64.7 + - - +
562B ILE* 3.2 6.9 + - - +
563B LEU* 2.8 40.8 + - + +
585B LEU* 4.6 2.7 - - + -
587B LEU* 3.9 10.1 - - + -
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Residues in contact with LYS 560 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555B LEU 3.2 5.7 + - - +
556B GLN* 3.1 36.3 - - + +
559B VAL* 1.3 85.9 - - - +
561B PRO* 1.3 67.5 - - + +
563B LEU* 3.2 4.6 + - - +
564B GLU* 3.1 52.9 + - + +
582B LEU* 4.4 3.0 - - + +
587B LEU* 2.8 47.7 + - + +
588B ALA* 4.2 7.9 + - - +
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Residues in contact with PRO 561 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556B GLN 3.3 12.8 - - - +
557B SER 3.2 15.0 - - - +
558B GLU* 3.0 20.2 - - - +
560B LYS* 1.3 96.7 - - + +
562B ILE* 1.3 62.0 + - + +
564B GLU* 3.3 14.8 + - - +
565B LYS* 3.1 22.7 + - - +
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Residues in contact with ILE 562 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525B LEU* 3.8 33.4 - - + +
528B ALA* 4.0 25.1 - - + -
539B VAL* 5.4 0.4 - - + -
543B LEU* 4.2 17.0 - - + -
558B GLU 3.3 16.2 - - - +
559B VAL* 3.2 8.4 + - - +
561B PRO* 1.3 78.8 - - + +
563B LEU* 1.3 62.8 + - - +
565B LYS* 3.0 33.9 + - + +
566B LEU* 3.2 13.3 + - + +
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Residues in contact with LEU 563 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540B ALA* 4.1 19.1 - - + -
543B LEU* 3.8 25.8 - - + -
559B VAL* 2.8 31.6 + - + +
560B LYS 3.6 3.6 - - - +
562B ILE* 1.3 73.8 - - - +
564B GLU* 1.3 62.2 + - - +
566B LEU* 3.2 18.1 + - + +
567B THR* 3.3 18.0 + - - +
578B ALA* 3.9 6.8 - - - +
581B ALA* 4.0 24.9 - - + -
582B LEU* 3.9 25.1 - - + -
585B LEU* 3.9 27.4 - - + -
587B LEU* 4.4 1.6 - - + -
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Residues in contact with GLU 564 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560B LYS* 3.1 46.6 + - - +
561B PRO* 3.7 14.4 - - - +
563B LEU* 1.3 70.6 - - - +
565B LYS* 1.3 61.7 + - - +
566B LEU 3.0 5.6 + - - -
567B THR* 2.9 23.8 + - - +
568B GLN* 3.2 16.8 + - - +
582B LEU* 4.1 20.3 - - + +
588B ALA* 5.6 0.5 - - - +
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Residues in contact with LYS 565 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528B ALA* 6.5 1.1 - - + -
561B PRO 3.1 12.2 + - - +
562B ILE* 3.0 28.1 + - + +
564B GLU* 1.3 77.9 - - - +
566B LEU* 1.3 60.0 + - + +
568B GLN* 2.9 30.5 + - - +
569B ASP* 3.4 22.4 + - - +
570B GLN* 4.9 1.9 + - - +
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Residues in contact with LEU 566 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528B ALA* 4.2 24.2 - - + +
536B ARG* 4.2 15.9 - - + +
539B VAL* 4.4 11.0 - - + -
540B ALA* 4.2 28.3 - - + +
562B ILE* 3.2 21.3 + - + +
563B LEU* 3.4 16.4 - - + +
564B GLU 3.0 0.6 - - - -
565B LYS* 1.3 80.2 - - + +
567B THR* 1.3 55.3 + - - +
568B GLN 2.9 13.9 + - - +
570B GLN* 4.7 7.9 + - + +
574B VAL* 2.7 49.4 - - + +
575B LYS* 3.8 0.2 - - - +
578B ALA* 3.7 8.3 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il